Update scripts to Python3

.travis.yml

@@ -15,7 +15,7 @@ addons:
     packages:
     - build-essential
     - cmake
-    - python
+    - python3
     - libboost-all-dev
     - libgsl-dev
     - libxerces-c-dev

CMakeLists.txt

@@ -2,13 +2,7 @@
 # Copyright © 2005-2013 Swiss Tropical Institute and Liverpool School Of Tropical Medicine
 # Licence: GNU General Public Licence version 2 or later (see COPYING)
 
-cmake_minimum_required (VERSION 2.4)
-# We still (try to) support cmake 2.4, but cmake 2.8 policies also work:
-if("${CMAKE_MAJOR_VERSION}.${CMAKE_MINOR_VERSION}" GREATER 2.6)
-    cmake_policy(VERSION 2.8)
-elseif("${CMAKE_MAJOR_VERSION}.${CMAKE_MINOR_VERSION}" GREATER 2.4)
-    cmake_policy(VERSION 2.6)
-endif("${CMAKE_MAJOR_VERSION}.${CMAKE_MINOR_VERSION}" GREATER 2.6)
+cmake_minimum_required (VERSION 3.0)
 
 project (OpenMalaria CXX)
 
@@ -94,6 +88,11 @@ find_package (XSD)
 find_package (XERCESC)
 find_package (GSL)
 find_package (Z)
+find_package (Python)
+
+if (NOT PYTHON_EXECUTABLE)
+    message (SEND_ERROR "Unable to find a Python interpreter (required).")
+endif (NOT PYTHON_EXECUTABLE)
 
 
 # Find Boost:

FindPython.cmake

@@ -4,7 +4,17 @@
 #
 # Defines PYTHON_EXECUTABLE. Doesn't abort if not found.
 
-find_program (PYTHON_EXECUTABLE python
+# We need Python 3.x which is now often the default version.
+# On Windows, install paths may help
+find_program (PYTHON_EXECUTABLE
+  NAMES python3 python3.exe python python.exe
+  PATHS
+    "C:\\Python37-x64" "C:\\Python37"
+    "C:\\Python36-x64" "C:\\Python36"
+    "C:\\Python35-x64" "C:\\Python35"
+    "C:\\Python34-x64" "C:\\Python34"
+    "C:\\Python33-x64" "C:\\Python33"
   DOC "Path to python (required).")
+message (STATUS "Found Python interpreter: ${PYTHON_EXECUTABLE}")
 
 mark_as_advanced (PYTHON_EXECUTABLE)

schema/CMakeLists.txt

@@ -2,8 +2,6 @@
 # Copyright © 2005-2011 Swiss Tropical Institute and Liverpool School Of Tropical Medicine
 # Licence: GNU General Public Licence version 2 or later (see COPYING)
 
-find_package (Python)
-
 set (SCHEMA_NAMES
   scenario
   demography

test/CMakeLists.txt

@@ -2,8 +2,6 @@
 # Copyright © 2005-2009 Swiss Tropical Institute and Liverpool School Of Tropical Medicine
 # Licence: GNU General Public Licence version 2 or later (see COPYING)
 
-find_package (Python)
-
 # Testing via run.sh or run.py script:
 configure_file (
   ${CMAKE_CURRENT_SOURCE_DIR}/run.py
@@ -53,14 +51,11 @@ set (OM_BOXTEST_NAMES
 # tests with broken checkpointing:
 set (OM_BOXTEST_NC_NAMES)
 # Disabled due to "in-progress" work: (none)
+
 # Use python script.
-if (PYTHON_EXECUTABLE)
-  foreach (TEST_NAME ${OM_BOXTEST_NAMES})
+foreach (TEST_NAME ${OM_BOXTEST_NAMES})
     add_test (${TEST_NAME} ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/run.py ${TEST_NAME} -- --checkpoint)
-  endforeach (TEST_NAME)
-  foreach (TEST_NAME ${OM_BOXTEST_NC_NAMES})
+endforeach (TEST_NAME)
+foreach (TEST_NAME ${OM_BOXTEST_NC_NAMES})
     add_test (${TEST_NAME} ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/run.py -- ${TEST_NAME})
-  endforeach (TEST_NAME)
-else (PYTHON_EXECUTABLE)
-  message(WARNING "Tests are disabled (Python is needed to run them)")
-endif (PYTHON_EXECUTABLE)
+endforeach (TEST_NAME)

test/run.py

@@ -1,4 +1,4 @@
-#!/usr/bin/python
+#!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 
 # This file is part of OpenMalaria.
@@ -51,7 +51,7 @@ def __str__(self):
 testSrcDir="@CMAKE_CURRENT_SOURCE_DIR@"
 testBuildDir="@CMAKE_CURRENT_BINARY_DIR@"
 if not os.path.isdir(testSrcDir) or not os.path.isdir(testBuildDir):
-    print "Don't run this script directly; configure CMake then use the version in the CMake build dir."
+    print("Don't run this script directly; configure CMake then use the version in the CMake build dir.")
     sys.exit(-1)
 
 # executable
@@ -106,7 +106,7 @@ def linkOrCopy (src, dest):
             # This can still fail: a VirtualBox guest is not allowed to create
             # links on a drive shared by the host
             os.symlink(os.path.abspath(src), dest)
-        except OSError,e:
+        except OSError as e:
             shutil.copy2(src, dest)
     else:
         shutil.copy2(src, dest)
@@ -133,13 +133,13 @@ def runScenario(options,omOptions,name):
         cmd=["xmllint","--noout","--schema",scenarioSchema,scenarioSrc]
         # alternative: ["xmlstarlet","val","-s",SCHEMA,scenarioSrc]
         if options.logging:
-            print "\033[0;32m  "+(" ".join(cmd))+"\033[0;00m"
+            print("\033[0;32m  "+(" ".join(cmd))+"\033[0;00m")
         return subprocess.call (cmd,cwd=testBuildDir)
 
     cmd=options.wrapArgs+[openMalariaExec,"--deprecation-warnings","--resource-path",os.path.abspath(testSrcDir),"--scenario",scenarioSrc]+omOptions
 
     if not options.run:
-        print "\033[0;32m  "+(" ".join(cmd))+"\033[0;00m"
+        print("\033[0;32m  "+(" ".join(cmd))+"\033[0;00m")
         return 0
 
     # Run from a temporary directory, so checkpoint files won't conflict
@@ -156,16 +156,16 @@ def runScenario(options,omOptions,name):
     linkOrCopy (scenarioSchema, scenario_xsd)
 
     if options.logging:
-        print time.strftime("\033[0;33m%a, %d %b %Y %H:%M:%S")+"\t\033[1;33m%s" % scenarioSrc
+        print(time.strftime("\033[0;33m%a, %d %b %Y %H:%M:%S")+"\t\033[1;33m%s" % scenarioSrc)
 
     startTime=lastTime=time.time()
     # While no output.txt file and cmd exits successfully:
     while (not os.path.isfile(outputFile)):
         if options.logging:
-            print "\033[0;32m  "+(" ".join(cmd))+"\033[0;00m"
+            print("\033[0;32m  "+(" ".join(cmd))+"\033[0;00m")
         ret=subprocess.call (cmd, shell=False, cwd=simDir)
         if ret != 0:
-            print "\033[1;31mNon-zero exit status: " + str(ret)
+            print("\033[1;31mNon-zero exit status: " + str(ret))
             break
 
         # check for output.txt.gz in place of output.txt and uncompress:
@@ -195,7 +195,7 @@ def runScenario(options,omOptions,name):
         lastTime=checkTime
 
     if ret == 0 and options.logging:
-        print "\033[0;33mDone in " + str(time.time()-startTime) + " seconds"
+        print("\033[0;33mDone in " + str(time.time()-startTime) + " seconds")
 
     if options.cleanup:
         os.remove(scenario_xsd)
@@ -218,7 +218,7 @@ def runScenario(options,omOptions,name):
                 ctsret,ctsident = compareCtsout.main (origCtsout, ctsoutFile)
             else:
                 ctsret,ctsident = 3,False
-                print "\033[1;31mNo original ctsout.txt to compare with."
+                print("\033[1;31mNo original ctsout.txt to compare with.")
             if ctsident and options.cleanup:
                 os.remove(ctsoutFile)
                 if os.path.isfile(newCtsout):
@@ -233,7 +233,7 @@ def runScenario(options,omOptions,name):
                 ret,ident = compareOutput.main (origOutput, outputFile, 0)
             else:
                 ret,ident = 3,False
-                print "\033[1;31mNo original output.txt to compare with."
+                print("\033[1;31mNo original output.txt to compare with.")
             if ident and options.cleanup:
                 os.remove(outputFile)
                 if os.path.isfile(newOutput):
@@ -243,12 +243,12 @@ def runScenario(options,omOptions,name):
             ret,ident = 1,False
             stderrFile=os.path.join(simDir,"stderr.txt")
             if os.path.isfile (stderrFile):
-                print "\033[1;31mNo output 'output.txt'; error messages:"
+                print("\033[1;31mNo output 'output.txt'; error messages:")
                 se = open(stderrFile)
                 se.read()
                 se.close()
             else:
-                print "\033[1;31mNo output 'output.txt'"
+                print("\033[1;31mNo output 'output.txt'")
 
         ret=max(ret,ctsret)
         ident=ident and ctsident
@@ -265,9 +265,9 @@ def runScenario(options,omOptions,name):
     try:
         os.rmdir(simDir)
     except OSError:
-        print "\033[0;31mDirectory %s not empty, so not deleted!" % simDir
+        print("\033[0;31mDirectory %s not empty, so not deleted!" % simDir)
 
-    print "\033[0;00m"
+    print("\033[0;00m")
     return ret
 
 def setWrapArgs(option, opt_str, value, parser, *args, **kwargs):
@@ -345,8 +345,8 @@ def main(args):
             retVal = r if retVal == 0 else retVal
 
         return retVal
-    except RunError,e:
-        print str(e)
+    except RunError as e:
+        print(str(e))
         return -1
 
 if __name__ == "__main__":

unittest/AgeGroupInterpolationSuite.py

@@ -1,4 +1,4 @@
-#!/usr/bin/python
+#!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 
 # This file is part of OpenMalaria.
@@ -52,7 +52,7 @@ def set_age_groups(self,age_lower_bounds,values):
         self.v=[values[0]]
         self.v.extend(values)
         self.v.append(values[len(values)-1])
-        print "Lengths:",len(self.a),len(self.v)
+        print("Lengths:",len(self.a),len(self.v))
 
     def interpolate(self,t):
         i=0
@@ -141,9 +141,9 @@ def plot(self,subplot):
 # Generate sample data for unittest:
 x=[15.2,18.09,7.0, 2.5, 0.0,20.0,900.0,62.0]
 
-print "Age points:",x
-print "Piecewise constant:",[const.interpolate(t) for t in x]
-print "Linear interpolation:",[linear.interpolate(t) for t in x]
+print("Age points:",x)
+print("Piecewise constant:",[const.interpolate(t) for t in x])
+print("Linear interpolation:",[linear.interpolate(t) for t in x])
 
 
 # Third plot: CMF data

unittest/CMakeLists.txt

@@ -2,8 +2,6 @@
 # Copyright © 2005-2009 Swiss Tropical Institute and Liverpool School Of Tropical Medicine
 # Licence: GNU General Public Licence version 2 or later (see COPYING)
 
-find_package (Python)
-
 set (OM_CXXTEST_INTERPRETER ${PYTHON_EXECUTABLE})
 set (OM_CXXTEST_SCRIPT ${CMAKE_SOURCE_DIR}/contrib/cxxtest/bin/cxxtestgen)
 
@@ -50,18 +48,13 @@ set (OM_CXXTEST_HEADERS
   PkPdComplianceSuite.h
 )
 
-#Appears to be problems with this on windows...
-if (OM_CXXTEST_INTERPRETER)
-  add_custom_command (OUTPUT tests.cpp
-    COMMAND ${OM_CXXTEST_INTERPRETER} ${OM_CXXTEST_SCRIPT} ${OM_CXXTEST_OPTIONS} --runner=ParenPrinter -o ${CMAKE_CURRENT_BINARY_DIR}/tests.cpp ${OM_CXXTEST_HEADERS}
+add_custom_command (OUTPUT tests.cpp
+    COMMAND ${PYTHON_EXECUTABLE} ${OM_CXXTEST_SCRIPT} ${OM_CXXTEST_OPTIONS} --runner=ParenPrinter -o ${CMAKE_CURRENT_BINARY_DIR}/tests.cpp ${OM_CXXTEST_HEADERS}
     DEPENDS ${OM_CXXTEST_HEADERS}
     WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
     COMMENT "Generating unittest code with cxxtestgen"
     VERBATIM
-  )
-else (OM_CXXTEST_INTERPRETER)
-  message (SEND_ERROR "Unable to find python executable. Thus I can't build tests.cpp which is required to run the unittests.")
-endif (OM_CXXTEST_INTERPRETER)
+)
 
 # These files are needed to run various infection model tests:
 configure_file (${CMAKE_SOURCE_DIR}/test/autoRegressionParameters.csv ${CMAKE_CURRENT_BINARY_DIR} COPYONLY)

unittest/DecayFunctionSuite.py

@@ -1,4 +1,4 @@
-#!/usr/bin/python
+#!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 
 # This file is part of OpenMalaria.